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Re-discovering his identity and humanity, Genra breaks from his cursed slavery from the evil DOATEC. Aiding his ninja allies raid on DOATEC, Genra heads to the Head Bio Core Lab, in which Alpha-152 is stored.
With his ninpo, super armor, double bladed energy sword and powers obtained from the Omega Project, Genra faces the cursed Alpha-152.

WHO SHALL WIN?

Alpha for a couple of reasons.

It was DOATEC's most important and dangerous project they created. The Alpha-152 project started if I recall before the events of DOA2.

Omega's force waves/shock waves is also something Alpha-152 has. His energy sword is made of pretty much the same material as Alpha's whole body. I don't see what harm the sword would do to it. Omega's attacks may fatigue her I assume, not that it has shown fatigue. Alpha fought Kasumi for a good while and was still fresh at the end.

Alpha is leaps faster and has effective teleportation and counters (I don't know if Omega can teleport despite in his human form was a Mugen Tenshin leader or something of that sort). Omega's energyballs/fireballs, whether medium or massive, can be dodged effectively by Alpha, especially considering its vast speed (when it departed from the battle against Kasumi in Helena's DOA4 ending) and its ability to fly.

Alpha wins mainly due to her speed and evasiveness. Omega may seem like a sitting duck in this what-if battle.